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[Microbiology] [3] [Cytoplasmic components] by [Dr. Boylan]

[20] [Example of a monomer of peptidoglycan
2 amino sugars and a tetra peptide T]
[Dr. Boylan] Some of you talked after the first class and asked about how to do the
attendance. So last night I sent an email (11:40) and I tried to clarify and so the
attendance is not a required as I said yesterday. Its totally up to you but I
recommend it. You come to lecture and study the materials and you do well. The
system here is that randomly I will take attendance. The way to do it was used to be
with a clicker (sometimes works and sometimes doesnt). I thought Id just
distribute the scantrons. Pick it up, write down your name, and then your E
numbers. If you want to write down your seat numbers thats fine. The E numbers is
key here. I will collect the scantron after the lecture. I wont collect in the middle if
there are 2 hours. After the lecture I will leave two boxes (one in the front and 1 in
the back and drop it there). Then we will do this counting. Again it is totally
randomly. This is to help students who really work hard and want to get extra
points in the course. If you have any questions feel free to email me or talk to your
curriculum representative.
Good afternoon, so how do we get that down. I like that. Dim the lights. Started off
talking about microbiology and 4 different microbes are included among that group.
The work of Pasteur and then we started to talk about bacteria and we discussed the
cell membrane and the functions that are carried on the membrane especially since
they dont have a lot of the organelles that they eukaryotes dont. Bacteria are
prokaryotes and are simple cells. They lack a nuclear membrane. They have a
nucleoid DNA. Other names of DNA bacteria are chromosome genome. Its replican
b/c it replicates. WE talked about its lengths and how its super coiled. Lets get back
to what I consider the most important feature (the cell wall) and heres a slide I
showed 2 days ago. The building block of peptidoglycan (made up of peptides and
glycans). We see here the two sugars. This one here is N-acetyl glucosamine. Its a
glucose molecule w/ a N-carboxyl group there molecule there. Its N-acetyl. Its an
amino sugar. This is the other amino sugar and is the same as this one except it has a
lactic acid group attached to it. That makes it a sugar called N-acetylmuramic acid.
These are two amino sugars that form the sugar backbone of peptidoglycan. Then
you have the peptide portion. The common one is L-alanine and D-glutamic acid
really, Lysine, and then D-alanine which is only found in bacterial cell wall. Lysine as
you recall is the amino acid thats (some word that I cant understand what he says
b/c he mumbled. I tried to slow it down and it didnt help) by DAP which looks like
Lysine but it has a one arm difference so go back and review that. If you look at the
backbone here, the glucosamine, muramic acid, etc. these paired sugars combine
over and over again to form a lattice around the whole cell. The dark circle
represents the Lysine or DAP. This would be the L-alanine as the #1 sugar, glutamic
acid #2, lysine #3, and D-alanine as #4.

[21] [Cross-linking in peptidoglycan]
[Dr. Boylan] Just to show it here again. Here we have the peptide bond (cross-
linking) formed. 1,2,3, here formed w/ the lysine in this peptide and the D-alanine of
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an adjacent peptide. Thats the peptide bond that keeps the peptidoglycan together
and forms this structural component. Preventing it from getting so large that it
would burst. Without the peptide bond shown there, there probably wouldnt be
any bacteria. Thats how important the bond is. Without peptidoglycan all cells
would lyse. In gram-positive bacteria you have layer after layer of peptidoglycan.
This goes around the whole cell. But cells have openings and pores so things can get
outside the bacterial cell (foods, metabolites, and all kinds of good things pass
through it to get into the interior of the cell where growth occurs). Dont just think
of it as a dense component where nothing can pass through.

[22] [Close-up of a type of bridge]
[Dr. Boylan] Heres that linkage again. Heres DAP. D-ala is the 3 so amino acid 3
and 4 on adjacent strands.

[23] [Cross-linking in peptidoglycan]
[Dr. Boylan] Here it is again. Anybody notice one thing different about the
peptidoglycan has shown in the lower part (B) that what we have seen in the
previous slides. Look at here. Ahhh which one. Here and here and here. So usually
the linkages are 4 amino acids (tetra peptides) but really when they are first
synthesized as peptidoglycans are being produced they are formed as pentapeptide
w/ two D-ala at the ends. Ala as #1, glutamic acid, DAP, D-ala, D-ala. The last D-ala is
cleaved and lost and the peptidoglycan is synthesized. Well show you why its an
important role that this is D-ala, D-ala peptide, well what the purpose of the
cleavage is later one. Initially its a pentapeptide and then it becomes a tetra peptide.
The last one is cleaved and lost for a very important function.

[24] [Example of another type of bridge
in Staphylococcus aureus (left)]
[Dr. Boylan] And one other type of linkage b/w peptidoglycan strands here were
talking about we see this type of already, (1,2,3,4) is that the one found in the
bacterium on S. aureus has a slightly unique linkage b/w its strands of
peptidoglycan in that it has 5 residues of glycine so glycine 1,2,3,4,5 complicating
things a bit. Heres the 1 strand, heres the lysine, heres the adjacent strand. But
between these two strands you have pentaglyciene (5 glycine) which is found in S.
aureus which will help the strands separate and arent as close together when they
have this gly bridge b/w them. There are all kinds of variation in bacteria but this
one is an important one.

[25] [Peptidoglycan - additional notes]
[Dr. Boylan] Peptidoglycan protects it from bursting and gives it the shape of the
cell. Its also the spot for the action of an enzyme lysozyme. Lets go back a couple
slides and we see that we mentioned it here. Heres the sugar backbone (2 amino
sugars) and see this linkage hydrolyzed by lysozyme. The sugar backbone of
peptidoglycan can be broken apart and destroyed by this enzyme known as
lysozyme. I dont know what that T up there means so forget about that. Lysozyme
what it does (its an enzyme and we have it in all our secretions in our body). This
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enzyme is one of our defenses against bacterial infections (host defenses against
bacterial infections). If we happen to pick up bacteria that is pathogenic and touch
our eye. Teardrops will have lysozyme in them, which will hopefully destroy the
bacteria by cleaving the sugars (the bond b/w the two amino sugars). I want to
point out that thats how that works. The linkage of the formation of the peptide
bonds b/w adjacent strands is carried out by transpeptidase called transpeptidation
and penicillin is the anti-biotic that inhibits the peptide bond b/w the strands of
peptide glycan. Penicillin is an antibiotic and is one of the best of all time. Bacteria
are becoming resistant to it. The wonder drug that saved so many thousand lives in
WWII, weve overused it. You hear problems about antibiotic resistant and they are
resistant to penicillin and other antibiotics. Its a wonder drug that works against
that particular bond of peptidoglycan.

[26] [No title]
[Dr. Boylan] There is much more peptidoglycan in cell walls of what we call gram-
positive bacteria than gram negative.

[27] [Teichoic acids]
[Dr. Boylan] Lets take at each of these in turn. We will first look at gram-positive
bacteria and then gram negative shortly. Positives cell wall is about 80%
peptidoglycan and negative is 15%. The cell wall of gram negative is only 15%
roughly peptidoglycan so a lot less. The only other major component in positive is
teichoic acid. Teichoic means wall in I think Greek. You remember in building blocks
and biochem that glycerol (3 carbon compound). Well there are two types of
teichoic acid. One of them is made up of glycerol linked to other glycerols over and
over again by a phosphorous. Glycerol phosphate, etc. Heres another large
macromolecule (t. acid) and you put these monomers together to put chain upon
chain of glycerol residues. In addition to that you have ribitol phosphate, which is
connected to other ones by ribitol phosphate. T. Acids are found in the wall and are
made up on glycerol or ribitol and they stick to the peptidoglycan for about 20% of
the wall. They have a strong negative charge, which is why the surface of the
bacteria has a strong negative charge. Well see the Importance of it later. The wall t.
acid as I just mentioned. Another type is the lipoteichoic acid we see here. These
stick right on up through the peptidoglycan. These strands originate in the cell
membrane. They are called lipoteichoic acids. This little part of them that is stuck
here is a lipid. Heres the lipid and heres the lipoteichoic acid going up. Its always
made up on glycerol phosphate never ribitol. So t. acid, wall t. acids, ribitols, or
glycerol phosphates residues and chains and that are found in the cell wall in the
peptidoglycan. The specific ones are lipoteichoic acids in the cell membranes and
they stick on through the peptidoglycan. Both of these t. acids are exterior. They
kind of poke up on top of the peptidoglycan. The rolls of t. acids are antigenic and
can be involved to adherence and they give a negative charge. Antigenic we will talk
about later. These t. acids do stimulate an immune response in us and they are
involved in adherence. Once again our friend staph. They have a lot of t. acids in
them to help them adhere and stick to our epithelial cells. These things are repeated
over and over again. S. aureus (we all have it on us) and they really like to live on
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our skin or in the anterior part of the nose where its a bit cooler. These S. aureus
use the t. acids to stick to the epithelial tissues in the front part of the nose.

[28] [Gram-negative wall components]
[Dr. Boylan] Heres a gram-negative cell wall. You can see its a bit more
complicated than a gram positive. Lets start off in the bottom here and work our
way up. This is cell envelope meaning membrane and wall together. Here we have
the cell membrane, the cytoplasmic membrane weve already discussed,
phospholipid bilayer, and proteins in it. Then we go up here and we see another
what we call outer membrane. So heres the layer of phospholipids but its only one
layer of phospholipids. Not a bilayer. In the outer part of that bilayer we have a
structure called LPS. Lipopolysaccharide. Thats the stuff thats right here which
goes through here and up like this. They make up the bulk of the outer leaflet. Heres
a double leaflet and another bilayer and only the inner leaflet is a bilayer. LPS also
known as endotoxin. Very important molecule b/c many times we have an infection
caused by gram negative bacteria, the LPS is responsible for the fever we get in
infections and it can also induce shock. The LPS can shut down organ function
leading to death. Its a very important biological molecule. Of course we have gram-
negative bacteria in our intestinal tract but thats the ok LPS that doesnt cause us
any harm. The one that causes infections can lead up to death b/c of the function of
the role of LPS. The next slide will show more detail about LPS. We have porins in
the outer membrane. Here we have the trimers (3 peptides that open and close and
once again regulate what passes through from the outside). Bacteria that grow have
to get food from the outside. They sometimes cant get large polysaccharides to pass
through into the interior so the porins can regulate the size of what passes through
from the exterior and works its way down into the cell interior. They restrict
passage of proteins through roughly 1,000 Daltons. Any molecules larger than that
will be restricted and prevented from passing through. Anything smaller than that
(sugar/ amino acids) can go through but anything larger, the cell needs to break
them down into smaller components. The space b/w the cell membrane and the
outer membrane are called the periplasmic space. Its this white here which is filled
w/ fluid. Space b/w the cell membrane and the outer membrane and this is where
you find peptidoglycan in gram-negative bacteria. Peptidoglycan shown here. You
can only see a monolayer in gram-negative bacteria in contrast to the multilayer in
gram-positive bacteria. It is needed and is found in the periplasm in gram negatives.
Then you have nutrient binding proteins. Here we have binding proteins shown
here. Some of these proteins are called PBPs for penicillin binding proteins and are
found in the periplasm of gram-negative bacteria. Lipoproteins are what bind the
peptidoglycan to the outer membrane preventing it from floating away. This is
essential the cell wall of a gram-negative bacterium.

[29] [LPS close-up]
[Dr. Boylan] Here are the LPS that we just saw before. Its called the endotoxin as
well. Once again its toxic which causes fever. The part that causes fever is the lipid
portion (lipid A). Thats all we want to know about that. There may be hundreds and
thousands of copies of LPS. The lipid portion is responsible for fever, hypertension,
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and shock in negative infections. There are 3 parts to LPS (#1- lipid A found in the
outer membrane, #2 core polysaccharide- 4,5 sugars (almost the same in all
negative bacteria), #3-o antigen shown here). Once again we have that familiar story
of repeating monomers. Look at this, 4 sugars that is synthesized by a gram negative
bacterium and then another unit is created and added on to the top of that over and
over and over again up to 40 unites for this sugar. Different bacterium makes
different combinations of sugars (thousands of types of o antigens). They have one
basic until of sugars though. In a way, the composition of sugars in o antigen helps
us identify in the lab different bacteria b/c the differences in the composition in the
o antigen. You can pretty much tell what genus/ species youre working with.

[30] [Cell wall-defective cells]
[Dr. Boylan] Cell wall defective cells. So far we have talked about the composition
of the positive/ negative walls but protoplasts are positive bacteria that have
completely lost their cell wall. If they lose their cell wall the cells will die and burst.
The will pop or burst. We have protoplast that are positive and have no cell wall at
all. How do they exist? Ordinarily there are some other factors that help prevent
them from bursting. If we have an infection from gram-positive bacteria and we
treat it with penicillin its going to destroy the peptidoglycan but one of these
bacteria is hiding in our tissues and they are stabilized in the environment of our
lung tissue. W/o a cell wall they might survive for a while and maybe even grow.
Protoplasts are gram positive w/o the wall and they survive. Whats the
consequence of that? Youve heard of infections that are recurrent and youre taking
antibiotics and you feel better but a few weeks later the infection comes back. Ya the
infection was treated successfully but you have a few bacteria that hid in tissue in
your body and when the penicillin was taken away they came out and they synthesis
all over again. You have a recurrent infection. Spehroplasts are negative that have
lost their peptidoglycan but still retain the outer membrane. Protoplasts are positive
and spheroplasts are negative both of which have lost peptidoglycan. W/
spheroplasts they survive even longer w/o the peptidoglycan. L-forms refer to
protoplast that continue to grow and divide. Once again if they are protected from
bursting they can grow for a while and L forms are the names of cells that do grow
w/o a cell wall. They have the capacity to grow a cell wall and eventually they will
and blossom and cause recurrent infections. Mycoplasmas are a genus of bacteria
that never has a cell wall. How does it survive w/o a peptidoglycan? It has sterols in
its cell membrane. Its not a hearty bacterium at all. It doesnt last long outside the
body but it can survive since it has sterols that make that membrane a bit tougher
than the other bacteria we know about it nature.

[31] [Capsule]
[Dr. Boylan] Now we are going to talk about something further exterior. The
capsule. The capsule is a nice name for the slime layer. Extracellular and not a part
of the cell envelope. A lot of bacteria but not all for what is called a capsule. Another
name for it is glycocalyx. Some microbiologists differentiate b/w the two but
essentially they are the same. They are made up of a polysaccharide sugar, which is
why its called a slime layer. The capsule forms around the bacteria. They can
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survive w/o it but when they do have it, they have many advantages that other
bacteria dont have. The composition is polysaccharide sugars and among the types
that have capsules there is different compositions. The exception to being
polysaccharide is bacillus anthraces. This is the one that causes anthrax. For some
reason during the evolution of it the capsule is not going to be polysaccharide but a
capsule of single glutamic acid (polymer of it). Its different from all other capsules.
The others are polysaccharide. The functions of the capsule. Never underestimate
the power of the capsule. Bacteria that have a capsule can be extremely pathogenic
causing many serious infections. Among them, most of the bacteria that cause
pneumonia have a capsule. Most of the meninges of the brain have a capsule as well.
A capsule helps bacteria become sever pathogens. Why does it help them? It
prevents these bacteria from being eaten or destroyed by our white blood cells. Our
white blood cells known as phagocytes. These white blood cells are constantly in
our blood looking for invaders. When they have this slimy capsule around them,
they can slip away. It is harder for these phagocytes to engulf. They are anti-
phagocytic (what capsules are). Prevent phagocytosis or destruction by white blood
cells or macrophages. Thats what helps them be so difficult to eradicate/ get rid of
when they start to cause an infection and produce these serious diseases. Another
goal of the capsule is that theres a polysaccharide layer that surrounds the bacteria
(you can see this large capsule around them) is dehydration prevention. Bacteria
want to survive and how do they keep going on? If someone has a severe case of
pneumonia and they cough up these bacteria. They lodge all of the place. While most
bacteria would die w/in minutes/ hours, but when they have capsules, this mucoid
polysaccharide slime layer doesnt dry up as fast. They arent desiccated as rapidly.
They can survive on surfaces for hours or days b/c they dont dry up due to the
capsule. Other bacteria w/o a capsule would not survive as long in the environment.
It helps them to keep going on and become transmitted from person to person. The
longer they can survive the more likely someone will touch the contaminated object
and pick up the bacteria. Glycocalyx w/ strep mutans is the bacterium responsible
for carries. Its found in the plaque on our teeth. These bacteria in plaque produce all
kinds of polysaccharides and capsules and other things to stick to our teeth and each
other as well. S. mutans is the culprit in caries and it uses a capsule made up of
dextrans and glucose which helps bond tenaciously to our enamel. Its tough to
brush them away b/c of the dextrin capsule it produces. Other bacteria are there as
well but thats the one that sticks to our teeth and does the damage.

[32] [Cytoplasmic components]
[Dr. Boylan] No we can go through some of these things since we have talked
about some already. Nucleoid is single and a coil thats a double helix. Made up of
DNA. Ribosomes, polysomes are a bunch linked to each other. Inclusions also
bacteria have that we will talk about as well.

[33] [Bacterial chromosome]
[Dr. Boylan] Chromosome. Haploid, circular, linked about a thousand times longer
than the cell. Base pairs can be up to 5 million. The way I remember is the number of
genes. How many genes can a bacterial cell have? E. Coli has about 4,500 genes in its
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chromosome. Some have more or less. How many genes do a human have? 23. We
use to think that we more but we only have 23,000 genes all together. Now we can
modify our genes a lot through genetics but if you look at genes itself 4,500 to
23,000 genes in humans. So heres bacterium w/ a nucleoid. Heres what happens
when you burst the cell releasing the stuff and you can see how much longer it is
than the cell (1000x more)

[34] [CHROMOSOME REPLICATION]
[Dr. Boylan] I have a quick question before I discuss this problem. We have
haploid chromosome that means one chromosome but its cut in a double helix
(coiled) and the origin. Heres the chromosome and this chromosome has started to
replicate. One chromosome to two. Mother cell will grow and divide into daughter
cells. Each needs an intact chromosome. This darker area represents the initial
strand so double strand. The blue represents the newly synthesized strand, which
started at the origin, and it begins to replicate the DNA into complementary strand.
Semi-conservative replication occurs. DNA is going to have one strand from the
mother and one new strand. It then goes around and once it gets to this point here
the whole chromosome will be replicated and thats the terminus. It begins at the
origin and ends at the terminus. Semi-conservative replication. This process of
replication in bacteria takes about 40 minutes to replicate its chromosome. A
around of replication takes 40 minutes. Not only that, but look at the way its going
on. It goes from 12 oclock and goes clockwise and counterclockwise. It goes in both
directions. That is caused bi-directional replication. We dont have that. Ours dont
divide that way. Speeds up the replication but it still takes 40 minutes. Heres the
question I want to pose. I mentioned before that some can divide in 20 minutes.
Heres a cell called a mother cell and in 20 minutes there are 2 daughter cells but
they have chromosomes. Wait you said it takes to replicate the chromosomes but
these cells divide in 20 minutes. How is that possible? That was asked for many
years. Some of you may want to think about that and we can talk about it the next
time we meet. There is a way this happens.

[35] [Plasmids - properties]
[Dr. Boylan] The plasmids closed loops and circular. Its made up of only DNA.
That means it has genes. There is a bacterial cell that has a chromosome stuck to a
protein. Here we have the extra chromosomal DNA (plasmid). These are extra genes
in the plasmid. This is and advantage. The properties these bacteria can get when
they are a host to a plasmid, they can have a profound effect on the life of a bacterial
cell and what happens to us during the course of an infection. Plasmid can allow
benefit for the bacterium and that means they are more dangerous to us. Extra
chromosomal and are autonomous meaning they replicate independently. When the
chromosome replicates the plasmid does but does it only its own. The size is 3-4%
of the chromosome and has 10-15 genes compared to the 4500 genes in the
chromosome. Copy number refers to the number of plasmids in the cell (up to 20).
There can be different types of plasmids in a cell. A bacterial cell may have 2-3
plasmids. Autonomous means they replicate on themselves. Dispensable means its
not needed for survival but just provide advantage. They are transmissible meaning
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they can be transmitted from one cell to another. They are contagious and is why
one type of gene (destruction of antibiotics) and at the same time they are being
transmitted among different bacterial populations. More are picking up plasmids
and more are being resistant to these antibiotics. R plasmids stand for resistance to
antibiotics. These genes here. Some are called R plasmids and these have genes that
make the cells resistant to antibiotics. Resistant that destroys penicillin or
tetracycline. There are other ways to become resistant but this is a major one.
Plasmids are also involved in recombinant DNA work. They play an important role
in the life of a bacterial cell. Recombinant DNA is used to produce drugs in a lab
setting.

[36] [Ribosomes]
[Dr. Boylan] Ribosomes are the sites of protein synthesis. In our cells they are
80S. Heres eukaryote and has 2 subunits which are 60S and 40S. Depending on how
far they move in a centrifuge w/ a solution in it you see how far down it goes. The
bigger they are the farther they go down into the centrifuge. When separated the
subunits have different shapes. The larger is 60S and the smaller is 40S. Bacterial
cells have 70S 50S, 30S. Youll see this again dealing w/ antibiotics. Bacterial cells
and our cells have ribosomal cells for protein synthesis. There is a difference in size
and composition. Some drugs can inhibit effect in bacteria b/c of the differences but
have little effect on our cells. Protein synthesis is an essential function in all living
cells but if you stop synthesis you will stop it from growing thats great for us. Our
healthy cells can keep functioning. 50S has 5S and 23S. The 30S has 16SRNA. I
mention that b/c if you want to identify it on a molecular level, 16S RNA is unique to
bacteria. Every bacterium has its own unique 16SRNA. The part of DNA that codes
for it is unique. You can identify it most specifically looking for 16S RNA or the gene
for it and youll know exactly what kind of bacterium it is. Polysomes are ribosomes
linked together and are sites of protein synthesis. Ive already mentioned the
importance of ribosomal sizes and antibiotics since they will only bind to bacterial
cells and stop protein synthesis by stopping them from growing or killing them.

[37] [Inclusions]
[Dr. Boylan] We talked about the ribosome and of course they are in the
cytoplasm inside synthesizing proteins. There may be 10,000 or more ribosomes
when they are growing rapidly. Thinking of a cell that grows and replicates every 20
minutes. Just think about how quickly it has to synthesize the organelles. Another
type of body found inside bacterial cells are inclusions. For the most part they are
storage or granules where bacteria can store materials that they would like to hang
on to and store them for a while. They dont need them right away but maybe in the
next day or hour they will need to call upon the reserves of nutrients of growth and
division. We know we will have 3 meals a day so therefor we can know how much to
eat. We dont have to stop ourselves thinking this may be our last meal. bacteria
dont know that. They will store nutrients and not eat them right away but maybe
the next day they wont be in the same environment so they can store stuff. They are
storing organic and inorganic materials. Lipids they store are polymers of beta-
hydroxybutyric acid. They can store sugars in granulose. They need the sugar for
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growth. Inorganic inclusion is called volutin or metachromatic granules. Those are
made up of phosphate for their nucleic acid synthesis. We always need to mention
that b/c we use to have labs and every time we had labs and do this stain using
methlylblue but when we added this stain to cells w/ volutin they would become
red. So metachromatic (stain would change to red when it would bind to
phosphate). V

[38] [Bacterial appendages
Flagella]
[Dr. Boylan] There are two appendages. Flagella and pilli. Flagella are for motility.
here is a cell w/ one flagellum. One of its ends or its poles. Along thing, wavy, for
motility. They are so thin you cannot see them using the light microscope under
normal staining conditions. They are too thin (than a bacterial cell). How do you see
them? Well, what we do in the lab if you want to look to see if it has a flagellum or
not, we coat the bacterium w/ a silver nitrate or a salt. We keep dumping salts on
the bacterial cell (on a microscope side). We keep dumping the salt on and it keeps
sticking to the flagella and eventually it looks bigger and is visible in even in a light
microscope. Its made up of flagellin monomer. Linked together to form a long
filamentous flagellum. As you can see here is a flagellum but what happens is that it
goes around within these bodies called basal bodies in green here. It rotates around
that. You can see it goes in a counter clockwise formation. They are found in the cell
membrane and wall of the membrane. It rotates through these bodies. We have
flagella in the sperm cells but they act in a wave like motion to move cells along but
the flagella act like a boat propeller. You see here the flagellum moves around in
these basal bodies. Its moving in a counterclockwise. We know that b/c people have
studied it. We stick the tips through glass slides to keep the bacteria in place and
then see, which way the bacteria rotate. We know that when bacteria are moving
they are going in a counterclockwise direction. Not in a whip like fashion as in
eukaryotes.

[39] [Role of flagella]
[Dr. Boylan] Bacteria exhibit chemotaxis. Taxis means movement in a chemical
gradient. A gradient of chemicals. Chemicals that are high conc. to low conc. They
like to move one-way to another and its the gradient of chemicals. What does that
mean? Well show you soon. Lets look at these lower figures. We have a beaker w/
some liquid in it. Some kind that we stick a capillary tube in. Whats going through to
come through this hollow tube from here to here? Well it says no attractant so
nothing that the bacteria will benefit/ is attracted to. Its not an attractant for
bacteria. So whats going to happen then when the bacterium over here is going and
moving around and is moving back and forth over and over again. It has an erratic
movement. It winds up over here. What was coming through the tube did not attract
the bacterium to come newer it so it moved away. You notice here that what
happens is, it moves over from this spot to this spot. Its thinking to itself if Im in a
better spot or worse spot than where I was. Then it stops and we move here, stop,
sense the environment and then it continues to move. When it stops you see the
flagella stick out. The point Im trying to make is that the flagella are moving in a
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counterclockwise direction and then they stop and they sense their environment.
Their flagella start to move in a clockwise direction. They are sensing their
environment and thinking is it better or worse. They are sensing on the receptors of
the surface. When they move, its called running. When the bacteria move they run.
Theyre moving along. When they stop to sense their environment they tumble. Lets
try this way lets try that way. On the left, the bacterium moves in an unusual
pattern. What happens now, and you put an attractant. Whats an attractant?
Glucose or another sugar. Something that its really attracted to. Something that it
can use to grow and wants to survive. Lets see the difference now in the way the
bacteria initially moves. It moves along stops here, and tumbles. Sensing this
environment and sees what the conc. of the attractant says. Im moving along here
and the conc. at this site is more than before so I move in that direction stopping and
sensing the environment until it moves in that direction. It doesnt move in a
straight fashion but back and forth. It eventually gets there. That helps the bacteria
in the body. The ones that want to cause infection want to borough into the tissue
and find sites where there are nutrients for us to grow. What will happen if there
were not an attractant but a repellant? Maybe using acetic acid. They would do the
same thing but they would be as far away from the repellant than normally. Either
way its a chemical gradient. You know here, the gradient is much more attracted in
this area as it is introduced in the beaker than it is here. It moves in a chemical
gradient from low to high and then it grows a lot better as a result. The same thing
happens in the body since it helps them borough in the tissues. Even flagella can be
appendages that help bacteria cause infection.

[40 [ARRANGEMENT OF FLAGELLA
(-trichous)]
[Dr. Boylan] Arrangement of flagella can be used to classify. Trichous means
flagella. Mono- means one flagella. Lopho- tuff of flagella. Amph-/ Peri- are all
around the cell. These are ways to characterize all of bacteria. Some of them have
one and some have tufts at both poles. This is another way to identify bacteria by
the arrangement of the flagella.

[41] [Flagella in spirochetes]
[Dr. Boylan] An unusual flagella is found in spirochetes that we talked about in
the first lecture. The flagella in them stays inside the periplasm. They stay within the
space in the cell membrane and outer membrane. It leads to a twisting rotating
motion (corkscrew). This helps the bacteria borough into the tissue. Its called
endoflagulation since they are inside the cells. It helps them rotate in that spiral
fashion. Here we have the flagellum inside. Heres the outer membrane and inner
membrane and its not sticking out.

[42] [Bacterial Appendages
Pilli]
[Dr. Boylan] Another this is pilli. We can see they are here. They are much shorter
and straighter than flagella. They are made up of proteins and the protein here is
pilin. Flagella are made up of flagelin. Their main function is to help adhere. In the
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infections disease they have to stick to something. The bacteria that have pilli are
the main source of adhesion. We talked before the capsule, which can help the
bacteria adhere, but the pilli thats their main function. Host colonization is when
one bacteria will stick to epithelial cells and say I like it here. Now I can grow and
double to form colonies over time. They form little colonies inside of us. Not just one
cell but they colonize. They are also there to help w/ biofilm formation where you
have mixtures of bacteria (100s of species) like dental plaque. Living film of bacteria
(30-40 species). They work together and grow and they use their pilli to adhere.
Biofilms are also formed in other parts of the body for infections. Importance for the
pilli is demonstrated here. This question is often in the boards is this. The
importance of the pilli is always on the gonococcus. It has pilli or fimbriae plus or
negative. If it has pilli its called Film+ and if it doesnt its called Flm-. If you get rid of
the pilli from gonococcus they will not be infectious at all. You can inject someone
with millions of it but if they dont have pilli they wont cause an infection. That
points out the importance of pilli. If they cant stick they are not going to cause and
infection. W/ gonorrhea they cant stick at all. There is a special pilus called the sex
pilli and its not shown here but its also protein pilus. Its a little bit larger than the
ones shown here well see what happens. The special pilus is formed as a sex pilus,
which helps bacteria stick to each other and mate. We will talk about this next week.
The combine and unite and having sex meaning they exchange their DNA. They do
this by the sex pilus. It helps the bacteria conjugate for the exchange of DNA.

[43] [Spores]
[Dr. Boylan] And then we have bacterial spores. Spores are bacterial cells. They
are also called endospores. They are called endospores because they are found
inside the bacterial cells. Just like endotoxin, well talk later about exotoxin. In
bacteria they are called spores or endospores. Later we will talk about spores or
fungi that are formed inside the cell. Only two types of genus produce spores,
Bacillus and clostridium. Positive bacteria, bacillus is a stripped aerobe and
clostridium is a gram positive as well and is anaerobic. Here we have two gram
positive rod bacterium which look the same. Both are gram positive and both form
spores. One can grow in the presence of oxygen but they can form spores. They are
growing anywhere in the body/ test tube and they grow for a while. All of a sudden
they sense they are running out of nutrients. They are going to starve. Most bacteria
will starve and will die. But not these two genera. Once they sense they are running
out of food they sense if there is a lot of carbon in the environment, nitrogen and as
they deplete their food they start to run out of the nutrients which they detect as a
reduction of carbon and nitrogen sources. They thus form spores so that they will
survive even when they run out of food. Spores in contrast in fungi are produced for
reproduction. Spores in fungi are for reproduction while in bacteria they are used
for survival. They can survive for hundreds of years. They are living bacterial cells
but they are completely inert. They dont carry out metabolism or grow. They are
viable and are alive but they dont carry out any kind of reactions inside. They are
metabolically inert. Properties of spores, they are dormant. They have resistance to
heat and chemicals. This is why they are important. They are resistant to heat and
chemicals. They are formed to survive and its possible later on that this inert form
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may begin to grow again. They are resistant to heat and chemicals. Heres a spore.
The interior portion is called the core. Spore, inert, no metabolism, but inside this
core is DNA, RN, enzymes, lipids, sugar, everything else it will need if it wants to
function as a normal bacterium again. Its resistant to heat and chemicals because
there is no water in the core. It is dehydrated. Think about why are our cells
destroyed when we boil them in water. Without any water in the core of these
spores even boiling water wont effect them. The other reason is so resistant to heat
b/c of the dipicolinic acid (just remember the name), which is often associated with
calcium. It forms up to 15% of the core. It also helps the spore becomes resistant to
heat. Lack of water, this acid, and calcium helps build resistance to heat. This is why
we have to special conditions to kill them. Lets not go through the other layers
except for the coat. Remember the core, acid, and protein coat. The coat is shown
here and it surrounds the core is a thick protein. Its a keratin like protein meaning it
is very thick. This coat protects the spore from the passage of chemicals from
outside to inside. This coat is a thick keratin like protein that makes the spore
chemical resistant. These are important traits that help spores survive. Whats the
problem if they are inert? They can come back and form normal active cells.

[44] [Spore components]
[Dr. Boylan] So we went through that already. Sporulation. Heres a bacterial cell
well see in the slide sensing its running out of food (triggering events). No carbon
or nitrogen and thus form spores to survive. Its a differentiation process meaning
that these bacteria always had the genes in their chromosomes to form spores. They
always had the genes but those genes as you know can be turned off or repressed. I
like it/ this is good for me so I dont need to form a spore. When it starts to run out
of food, I will form a spore and I will survive. It turns off a gene and turns on other
genes. A whole bunch of genes in this bacteria are always there but then they are
repressed. Turning off that they were using before and turn on the genes for
repression.

[45] [Sporulation and germination]
[Dr. Boylan] Here we have the growth and preparation just to show that spores
are formed. Here we can see the spore is formed. This is just normal growth. It
begins to divide. Notice that the septum is closer to one end and not in the middle as
normal division. The spore is forming inside the cell (endospore). DNA, RNA,
proteins, enzymes. Lose water and form the coat and others and finally the intact
spore is formed inside the cell. The cell lyses releasing a free spore. This is the living
inert dormant cell resistance to heat chemicals. As said before it can survive for
maybe 100s of years. Sometimes it comes back to life. Its kind of like a chick coming
out of an egg cell. Under the right circumstances, sensing its environment.
Somebody drop these spores in a nice rich carbon broth environment. Lets break
out of this shell and emerge. They can germinate and grow once again as normal
bacterial cells. One cell that comes out can multiply into thousands and millions of
cells from a spore. 1 cell 1 spore 1 cell millions of other cells. One more term
I could use. You talk about these other cells called vegetative cells. All bacteria are
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bacteria cells in contrast to spores that are unique. A vegetative cell pops out and
grows out over and over and over again.

[46] [Review]
[Dr. Boylan] Review. Some properties of positive and negative cells. Can be seen
b/c of the composition of their cell wall. The gram stain is an important distinction
for these cells. Outer membrane only in negative. Cell wall and thicker proteoglycan
in positive. 80% here and 15% here. LPS only in negative. Endotoxin only in
negative (just like LPS). T. acid never found in the negative bacteria. If you had a test
looking for a t. acid youd know it was positive if the test was positive. If you had
something that identified LPS you know its negative since only negative have it.
Sporulation only see in in positive. Not all bacteria have a capsule in causing
infection. Lysozyme. Sensitive I wouldnt completely agree w/ this statement. Its an
enzyme not an antibiotic. It cleaves the sugar bonds. Gram negative bacteria have
peptidoglycan but less so they are only partially sensitive to lysozyme. They wont
have a serious effect on negatives as they do on gram positives. The cell will then
lyse. The same regions penicillin acts on positive more than negative. We will see a
lot of infections that are treated w/ penicillin. It doesnt mean the negative bacteria
are completely resistant to penicillin.

[47] [Review 2]
[Dr. Boylan] If you just want to go through and see the differences we discussed. I
think we went over all of these things. Porins, capsule.

[48] [Comparison of viruses, bacteria and fungi]
[Dr. Boylan] We will talk next week about viruses too. Looking at the three major
microbes lets just give you a preview of their differences. Lets just look only at
bacteria. Living cells, they can grow as living cells. Size is 1-5 um. Both types of
nucleic acid. No mitochondria, rigid cell wall. They divide by binary fission. Viruses:
cells? No. They are not alive. They cannot reproduce on their own. They are not
cells. Smaller than bacteria. They do not have both types of nucleic acids. They either
have DNA or RNA. No nucleus, mitochondria, or ribosomes. They are not motile or
divide by binary fission. Fungi are neat cells. Larger than bacteria. Eukaryotes. Why
are they eukaryotes and not prokaryotes? They have a nuclear membrane. Large
ribosomes, rigid cell wall, and they divide by budding and mitosis. Just a preview of
the difference we be discussing.